## [1] "O77_p4_con_R1_2.hicup.bam"

Truncation & Mapping

Truncation Frequency

Category Read 1 Read 2
Total 68,437,598 68,437,598
Not Truncated 38,537,742 40,669,996
Truncated 29,899,856 27,767,602

Truncated Read Length

Category Read 1 Read 2
Average Length Truncated 47.4 47

Mapping Efficiency

Category Read 1 Read 2
Too Short To Map 4,568,809 4,822,896
Unique Alignments 58,424,592 56,921,482
Multiple Alignments 2,500,650 2,588,830
Failed To Align 2,943,547 4,104,390
Paired 49,035,064 49,035,064

Truncation and Mapping Bar Plot

Filtering

Filtering Breakdown by Category

Category Count
Valid Pairs 25,041,457
Invalid Pairs 23,993,607
Same Circularised 30,005
Same Dangling Ends 3,907,025
Same Fragment Internal 10,936,094
Re Ligation 6,639,247
Contiguous Sequence 270,646
Wrong Size 2,210,590
Total Pairs 49,035,064

Filtering Breakdown Pie Chart

Ditag Length Distribution

Frequency Line Plot

Deduplication

Deduplication Summary Table

Category All Ditags Unique Ditags
Read Pairs 25,041,457 35,040
Cis-close (<10Kbp) 2,000,586 3,044
Cis-far (>10Kbp) 14,782,729 18,375
Trans 8,258,142 13,621

Deduplication Bar Chart

Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data

Babraham Bioinformatics